Merge pull request #788 from JoostJM/circle-ci-mac-os

Fix errors in continuous integration

.circleci/config.yml

@@ -2,7 +2,7 @@
 # docker pull circleci/picard
 # docker run -it --rm -v /var/run/docker.sock:/var/run/docker.sock -v $(pwd):$(pwd) -v ~/.circleci/:/root/.circleci --workdir $(pwd) circleci/picard circleci build
 
-version: 2
+version: 2.1
 jobs:
   test-notebooks:
     working_directory: /pyradiomics
@@ -32,10 +32,72 @@ jobs:
           command: |
             jupyter nbconvert --ExecutePreprocessor.kernel_name=python3 --ExecutePreprocessor.timeout=-1 --to notebook --output-dir /tmp --execute  notebooks/helloRadiomics.ipynb notebooks/helloFeatureClass.ipynb notebooks/PyRadiomicsExample.ipynb
 
-  build-3.5: &build_template
+  build-mac-37: &build_mac_template
+    working_directory: ~/pyradiomics
+    macos:
+      xcode: 12.5.1
+    environment:
+      PYTHON_VERSION: 3.7.10
+      PYTHON_SHORT_VERSION: 3.7
+    steps:
+      - run:
+          name: Setup MAC OS environment
+          # Workaround the following error occurring because python installation is cached but gettext dependency is not
+          #   dyld: Library not loaded: /usr/local/opt/gettext/lib/libintl.8.dylib
+          #     Referenced from: /Users/travis/.pyenv/versions/3.7.2/bin/python
+          #     Reason: Incompatible library version: python requires version 11.0.0 or later, but libintl.8.dylib provides version 10.0.0
+          # See https://github.com/scikit-build/cmake-python-distributions/issues/112 and
+          # https://github.com/scikit-build/cmake-python-distributions/pull/113
+          command: |
+            echo "HOMEBREW_NO_AUTO_UPDATE=1" >> $BASH_ENV
+            brew install gettext
+            brew install pyenv
+            echo 'export PATH=$HOME/.pyenv/versions/$PYTHON_VERSION/bin:$HOME/bin:$PATH' >> $BASH_ENV
+            mkdir -p $HOME/bin
+            ln -s $(which pip3) $HOME/bin/pip
+            ln -s $(which python3) $HOME/bin/python
+            pyenv install --list
+            pyenv install $PYTHON_VERSION
+      - run:
+          name: Setup SciKit-CI
+          command: |
+            pip install scikit-ci scikit-ci-addons
+            ci_addons --install ../addons
+      - run:
+          name: Setup PyEnv
+          command: python ../addons/travis/install_pyenv.py
+      - checkout
+      - attach_workspace:
+          at: ~/pyradiomics
+      - run:
+          name: Install
+          command: ci install
+      - run:
+          name: Test
+          command: ci test
+      - run:
+          name: Build Distribution
+          command: ci after_test
+      - persist_to_workspace:
+          root: .
+          paths: [dist]
+
+  build-mac-38:
+    <<: *build_mac_template
+    environment:
+      PYTHON_VERSION: 3.8.10
+      PYTHON_SHORT_VERSION: 3.7
+
+  build-mac-39:
+    <<: *build_mac_template
+    environment:
+      PYTHON_VERSION: 3.9.5
+      PYTHON_SHORT_VERSION: 3.9
+
+  build-37: &build_template
     working_directory: /pyradiomics
     docker:
-      - image: circleci/python:3.5-jessie
+      - image: cimg/python:3.7
         user: root
     steps:
       - checkout
@@ -57,43 +119,89 @@ jobs:
           command: ci after_test
       - persist_to_workspace:
           root: .
-          paths: dist
+          paths: [dist]
 
-  build-3.6:
+  build-38:
     <<: *build_template
     docker:
-      - image: circleci/python:3.6-jessie
+      - image: cimg/python:3.8
         user: root
 
-  build-3.7:
+  build-39:
     <<: *build_template
     docker:
-    - image: circleci/python:3.7
-      user: root
+      - image: cimg/python:3.9
+        user: root
+
+  test_deploy:
+    working_directory: /pyradiomics
+    docker:
+      - image: cimg/python:3.8
+        user: root
+    steps:
+      - run:
+          name: Check Repo User
+          command: if [[ $CIRCLE_PROJECT_USERNAME != "AIM-Harvard" ]]; then circleci step halt; fi
+      - checkout
+      - run:
+          name: Setup SciKit-CI
+          command: |
+            pip install scikit-ci scikit-ci-addons
+            ci_addons --install ../addons
+      - run:
+          name: Install
+          command: ci install
+      - run:
+          name: Install patchelf auditwheel, twine
+          command: |
+            apt update
+            apt-get install patchelf  # needed to run auditwheel
+            python -m pip install "auditwheel<3.2.0"
+            python -m pip install twine
+      # only attach the workspace at this point to prevent the removal of source distributions
+      - attach_workspace:
+          at: /pyradiomics
+      - run:
+          name: Create sdist
+          command: python setup.py sdist
+      - run:
+          name: Fix Distribution Wheels
+          command: |
+            ls ./dist/*-linux_$(uname -m).whl  # This will prevent further deployment if no wheels are found
+            # Since there are no external shared libraries to bundle into the wheels
+            # this step will fixup the wheel switching from 'linux' to 'manylinux1' tag
+            for whl in $(ls ./dist/*-linux_$(uname -m).whl); do
+                python -m auditwheel repair $whl -w ./dist/
+                rm $whl
+            done
+      - run:
+          name: Deploy source and linux wheels
+          command: python -m twine upload ./dist/*.whl ./dist/*.tar.gz -u $PYPI_TEST_USER -p $PYPI_TEST_PASSWORD -r testpypi
 
   deploy:
     working_directory: /pyradiomics
     docker:
-      - image: circleci/python:3.6-jessie
+      - image: cimg/python:3.6
         user: root
     steps:
       - run:
           name: Check Repo User
-          command: if [[ $CIRCLE_PROJECT_USERNAME != "Radiomics" ]]; then circleci step halt; fi
+          command: if [[ $CIRCLE_PROJECT_USERNAME != "AIM-Harvard" ]]; then circleci step halt; fi
       - checkout
       - run:
           name: Setup SciKit-CI
           command: |
-            pip install scikit-ci==0.13.0 scikit-ci-addons==0.11.0
+            pip install scikit-ci scikit-ci-addons
             ci_addons --install ../addons
       - run:
           name: Install
           command: ci install
       - run:
           name: Install patchelf auditwheel, twine
           command: |
+            apt update
             apt-get install patchelf  # needed to run auditwheel
-            python -m pip install auditwheel
+            python -m pip install "auditwheel<3.2.0"
             python -m pip install twine
       # only attach the workspace at this point to prevent the removal of source distributions
       - attach_workspace:
@@ -108,22 +216,22 @@ jobs:
             # Since there are no external shared libraries to bundle into the wheels
             # this step will fixup the wheel switching from 'linux' to 'manylinux1' tag
             for whl in $(ls ./dist/*-linux_$(uname -m).whl); do
-                auditwheel repair $whl -w ./dist/
+                python -m auditwheel repair $whl -w ./dist/
                 rm $whl
             done
       - run:
           name: Deploy source and linux wheels
-          command: twine upload ./dist/*.whl ./dist/*.tar.gz -u $PYPI_USER -p $PYPI_PASSWORD
+          command: python -m twine upload ./dist/*.whl ./dist/*.tar.gz -u $PYPI_USER -p $PYPI_PASSWORD
 
   deploy_conda:
     working_directory: /pyradiomics
     docker:
-      - image: circleci/python:3.6-jessie
+      - image: cimg/python:3.8
         user: root
     steps:
       - run:
           name: Check Repo User
-          command: if [[ $CIRCLE_PROJECT_USERNAME != "Radiomics" ]]; then circleci step halt; fi
+          command: if [[ $CIRCLE_PROJECT_USERNAME != "AIM-Harvard" ]]; then circleci step halt; fi
       - checkout
       - run:
           name: Install Miniconda
@@ -141,9 +249,10 @@ jobs:
           name: Build Conda packages
           command: |
             mkdir  /conda-bld
-            conda build ./conda --python=3.5 --croot /conda-bld
             conda build ./conda --python=3.6 --croot /conda-bld
             conda build ./conda --python=3.7 --croot /conda-bld
+            conda build ./conda --python=3.8 --croot /conda-bld
+            conda build ./conda --python=3.9 --croot /conda-bld
       - run:
           name: Deploy Conda packages
           command: |
@@ -153,31 +262,53 @@ workflows:
   version: 2
   build_and_deploy:
     jobs:
-      - build-3.5: &build_job_template
+      - build-mac-37: &build_job_template
           filters:
             tags:
               only:
-                - /^v?[0-9]+(\.[0-9]+)*(rc[0-9]+)?/
-      - build-3.6:
+                - /^v?[0-9]+(\.[0-9]+)*((a|b|rc)[0-9]+)?/
+      - build-mac-38:
           <<: *build_job_template
-      - build-3.7:
+      - build-mac-39:
           <<: *build_job_template
-      - test-notebooks:
-          requires:
-            - build-3.5
-            - build-3.6
-            - build-3.7
-      - deploy: &deploy_template
+      - build-37:
+          <<: *build_job_template
+      - build-38:
+          <<: *build_job_template
+      - build-39:
+          <<: *build_job_template
+      - test-notebooks: &requires_template
           requires:
-            - build-3.5
-            - build-3.6
-            - build-3.7
+            - build-37
+            - build-38
+            - build-39
+            - build-mac-37
+            - build-mac-38
+            - build-mac-39
+      - test_deploy:
+          <<: *requires_template
           filters:
             branches:
               ignore:
                 - /.*/
             tags:
               only:
-                - /^v?[0-9]+(\.[0-9]+)*(rc[0-9]+)?/
+                - /^v?[0-9]+(\.[0-9]+)*((a|b|rc)[0-9]+)/
+      - deploy:
+          <<: *requires_template
+          filters:
+            branches:
+              ignore:
+                - /.*/
+            tags:
+              only:
+                - /^v?[0-9]+(\.[0-9]+)*/
       - deploy_conda:
-          <<: *deploy_template
+          <<: *requires_template
+          filters:
+            branches:
+              ignore:
+                - /.*/
+            tags:
+              only:
+                - /^v?[0-9]+(\.[0-9]+)*((a|b|rc)[0-9]+)?/

MANIFEST.in

@@ -6,7 +6,7 @@ include requirements-dev.txt
 include requirements-setup.txt
 include versioneer.py
 
-recursive-include radiomics *
+recursive-include src/radiomics *
 
 recursive-include data/baseline *
 recursive-include data *_image.nrrd
@@ -24,4 +24,3 @@ recursive-include bin *.py
 
 recursive-exclude * __pycache__
 recursive-exclude * *.py[cod]
-recursive-exclude * nosetests.xml